net.maizegenetics.analysis.modelfitter

Interface AdditiveSite

All Known Implementing Classes:

AbstractAdditiveSite, GenotypeAdditiveSite, RefProbAdditiveSite

public AdditiveSite

Method Detail

getCovariate

kotlin.Array[] getCovariate()

Returns:

org.jetbrains.dokka.NodeRenderContent@f9df51c: the covariate for this site

getCovariate

kotlin.Array[] getCovariate(kotlin.Array[] subset)

Parameters:

subset - an int array indexing a subset of taxa

Returns:

org.jetbrains.dokka.NodeRenderContent@131ce975: the covariate for the subset of taxa for this sites

siteNumber

int siteNumber()

Returns:

org.jetbrains.dokka.NodeRenderContent@3b3a7a42: the site index corresponding to the site number in the source GenotypeTable

chromosomeName

java.lang.String chromosomeName()

Returns:

org.jetbrains.dokka.NodeRenderContent@7df04c07: the name of the chromosome of this site

position

int position()

Returns:

org.jetbrains.dokka.NodeRenderContent@1d2563b0: the chromosomal position of this site

siteName

java.lang.String siteName()

Returns:

org.jetbrains.dokka.NodeRenderContent@69866620: the name (SNPID) of this site

criterionValue

double criterionValue()

Returns:

org.jetbrains.dokka.NodeRenderContent@186e938: the value of the selection criterion for this site

criterionValue

void criterionValue(double value)

Parameters:

value - the value of the selection criterion for this site

selectionCriterion

net.maizegenetics.analysis.modelfitter.AdditiveSite.CRITERION selectionCriterion()

Returns:

org.jetbrains.dokka.NodeRenderContent@7ee91d7b: the selection criterion used for this site

reindexTaxa

void reindexTaxa(kotlin.Array[] taxaIndex,
                 java.util.List<java.lang.Integer> uniqueTaxa)

This method re-indexes the taxa in the additive site so that the returned covariate will match the taxon order in the target phenotype

Parameters:

taxaIndex - an index of taxa that matches the order in the target phenotype

uniqueTaxa - a unique list of index values used to recalculate major allele frequency for the taxa indexed

copy

AdditiveSite copy()

Returns:

org.jetbrains.dokka.NodeRenderContent@4867c9f5: a copy of this AdditiveSite